Juna, a high school student who does traditional Japanese archery, is riding along the seaside on her friend Tokio's motorcycle when they get into a mysterious accident and she dies. As her spirit floats away, a boy stops her and tells her he will grant her a second life if she will fight to defend the Earth from the strange 'worms' called Raaja. We also meet the mysterious organization SEED, who are on scene at a disaster involving the Raaja at a nuclear power plant.

Juna and Tokio return to the city and meet up with their classmate Saiyuri, while Teresa informs her SEED commander of a virus that's spreading over western Japan from genetically engineered agriculture. At a fast food restaurant, Juna learns one the perils of her new power, but all this is overshadowed when Tokio contracts the virus. Juna is sent into Tokio to save his life from the Raaja that lurks within both of them.